# Re: [AMBER] CPPTRAJ-Angle between two Helices

From: Jag Silwal <jagsilwal.gmail.com>
Date: Fri, 19 Jan 2018 16:17:03 -0500

Dan,

Thanks for your email. I will give it a try. I will also try in another
protein to verify this.

But am I using the mask correctly here? Basically, I am trying to
calculate the angle between two helices by choosing a common atom (2316)
from the loop region that connects two helices. Is this how its commonly
done? I just wanted to make sure I am correct on this one before I do other
calculations.

Thank you again!!

Sincerely,
Jag

On Fri, Jan 19, 2018 at 3:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Tough to really say what might be going on here without seeing the
> system. One thing I like to do in these situations is actually
> visualize the vectors themselves. You can do this by writing the
> vector data out in 'vectraj' (vector pseudo-trajectory) format, like
> so:
>
> vector Helix1 .2018 @2316
> vector Helix2 .2316 @22841
> run
> writedata vectors.nc vectraj Helix1 Helix2 trajfmt netcdf parmout
> vectors.parm7
>
> Then you can visualize what the 'vector' commands are actually
> calculating and see if those are good representations of your helices.
>
> Hope this helps,
>
> -Dan
>
> On Fri, Jan 19, 2018 at 1:23 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
> > Dear all,
> > I want to measure the angle between two helices in a protein for the
> > entire simulation (angle Vs time). I found the following guide from Dan
> and
> > I followed it and ran a sample run for one of the helices. I got the
> > results and everything but the angle is almost double what I was
> expecting
> > for the entire run.
> > So, I think I mightn't be using 'atom mask' properly here. So the two
> > helices are connected by a small loop with the turn of about 50 degrees.
> If
> > the starting of one helix is residue 'A' then turns at residue 'B' and
> > continues as another helix which ends at residue 'C', can I use the mask
> as
> > follows:
> > vector Helix1 .2018 @2316
> > vector Helix2 .2316 @22841
> > Where, *the numbers are the C-alpha atom number for residues A, B and C.*
> >
> > Did I do this right?
> >
> > Any insight would be helpful.
> >
> > Sincerely,
> > Jag
> > ............................................................
> ............................................................
> ...............
> > One thing you can try is calculating the angle between the vectors that
> run
> > along the helices; this can be done with cpptraj. First, read in your
> > topology and trajectory:
> > parm MyParm.parm7
> > trajin MyTraj.nc <https://www.researchgate.net/
> deref/http%3A%2F%2FMyTraj.nc>
> > Then you would create the vectors:
> > Then you can use the 'vectormath' analysis command to calculate the angle
> > between the vectors:
> > vectormath vec1 Helix1 vec2 Helix2 dotangle out H1-H2-angle.dat
> > Hope this helps,
> > -Dan
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jan 19 2018 - 13:30:04 PST
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